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I find the tab-delimited waypoint list files used in mavlink to be hard to read, so I added Protocol Buffer text format to the formats that mavwp.py can read and write.

I still think it can be improved to be even easier to read, but here's my current version of the mission defined in ardupilot-mega/Tools/autotest/mission2.txt:

QGC WPL PB 110
defaults {
  # Default coordinate frame for this mission.
  frame: FRAME_GLOBAL_RELATIVE_ALT
}
waypoint {
  command: CMD_NAV_WAYPOINT
  x: -35.362881
  y: 149.165222
  z: 582.0
}
waypoint {
  command: CMD_NAV_TAKEOFF
  x: -35.362881
  y: 149.165222
  z: 20.0
}
waypoint {
  command: CMD_NAV_WAYPOINT
  param2: 3.0
  x: -35.363949
  y: 149.164151
  z: 20.0
}
waypoint {
  command: CMD_CONDITION_YAW
  param1: 640.0
  param2: 20.0
  param3: 1.0
  param4: 1.0
}
waypoint {
  command: CMD_NAV_LOITER_TIME
  param1: 35.0
  param4: 1.0
  x: 0.0
  y: 0.0
  z: 20.0
}
waypoint {
  command: CMD_NAV_WAYPOINT
  param2: 3.0
  x: -35.363287
  y: 149.164958
  z: 20.0
}
waypoint {
  command: CMD_NAV_WAYPOINT
  param2: 3.0
  x: -35.364865
  y: 149.164952
  z: 20.0
}
waypoint {
  command: CMD_CONDITION_DISTANCE
  param1: 100.0
}
waypoint {
  command: CMD_CONDITION_CHANGE_ALT
  z: 40.0
}
waypoint {
  command: CMD_NAV_WAYPOINT
  param2: 3.0
  x: -35.363165
  y: 149.163905
  z: 20.0
}
waypoint {
  command: CMD_NAV_WAYPOINT
  param2: 3.0
  x: -35.363611
  y: 149.163583
  z: 20.0
}
waypoint {
  command: CMD_DO_JUMP 
  param1: 11.0
  param2: 3.0
}
waypoint {
  command: CMD_NAV_RETURN_TO_LAUNCH
}
waypoint {
  command: CMD_NAV_LAND
}